The show starts off with the build up from last season's cliffhanger revolving around Cartman's paternal origins. However, just as it seems they are about to get on with the second half of "Cartman's Mom Is A Dirty Slut," they do a 180 degree turn-around and reveal that for April Fool's Day they will be showing Terrance & Phillip in "Not Without My Anus."
Dr. Mephisto is about to reveal who Eric Cartman's father really is! Glass shatters and gunshots ring out. A mysterious assailant apparently shot Mephisto while the lights were off. Much to Eric's chagrin, they rush Mephisto off to the hospital. Chef rushes out the door with Mephisto in hand. They must fight against time to learn Eric's background, who is his father? Where does he come from?
The Booktastic bus is in town and soon everyone finds out that Officer Barbrady can't read. He is whisked off to school with the boys so he can save his job. While he's there someone in South Park is having sex with the town's chickens and only Officer Barbrady with his new deputies Kenny, Kyle, Stan, and Cartman can stop them!
Ike's going to have a Briss and everyone is invited! Stan, Kenny, and Cartman find out what a Briss really is and try to warn Kyle that his parents are going to cut off Ike's wee wee. Kyle sends Ike away to protect him from his scissor wielding parents.
Kyle is injured and must go to see the school nurse and is terrified because of the stories he's heard. She looks fairly normal, except for the dead fetus sticking out of her head. Kyle's mother educates the boys on her "condition" and decides that everyone in South Park should be made aware. Meanwhile, the South Park Cows dodgeball team goes to the state, national and finally the international finals in China.
Mr. Garrison assigns the boys to learn about Vietnam from somebody they know. Stan's Uncle Jimbo and his friend Ned tell the boys their outrageous tale. Mr. Garrison doesn't believe the boy's report and gives them detention. They plot revenge against Stan's Uncle by submitting a phony video of the Mexican Staring Frog of Southern Sri Lanka to them.
While their school bus is dangling on the edge of a cliff, the boys remember some of their past adventures. Mrs. Crabtree catches a ride into town with a stranger and winds up doing a brief stint as a standup comedienne. Back in South Park, Mr. Mackey convinces the parents that their missing children must have run away. In the end it's all a dream within a dream.
Schools out for summer and with Mr. Hat missing, Mr. Garrison is over the edge. The state has a ban on the sale of fireworks, and it screws up the boy's plans for a 4th of July celebration. Mr. Garrison seeks psychiatric help from Dr. Katz while Jimbo and Ned go to Mexico, in an attempt to smuggle fireworks back to the children of America.
A film festival moves to South Park, only to have a devastating effect on the sewer system. Mr. Hankey calls upon Kyle for help. The movie people interpret Kyle's pleading as a pitch and they quickly turn his story into a film starring Tom Hanks and a monkey they call "Mr. Hankey." Kyle is outraged that the filmmakers aren't hearing his pleas. Soon Chef's Salty Chocolate Balls energizes everyone.
Cartman's mother plots to give the boys the chickenpox by sending them over to Kenny's for a sleepover. Both Stan and Cartman breakout, but Kyle remains immune. Kyle discovers "the parental conspiracy" and with the other boys hires a prostitute to give their parents herpes. Meanwhile, Kenny's mother and Kyle's mother reunite their husbands who were both childhood friends that drifted apart.
The kids go on a field trip to the planetarium. All of the children except Cartman are acting weird. As usual Stan and Kyle, with Kenny's sacrifice, try to get to bottom of the mystery. Meanwhile, Cartman wins an appearance on a snack commercial. The four boys get to the root of the strange planetarium.
Stan needs to build a clubhouse so he and Kyle can play "Truth or Dare" with Wendy and her friend, who has a crush on Kyle. Cartman and Kenny retaliate by building a clubhouse of their own; only theirs has hot chicks. Meanwhile, the Marshes marriage breaks up and Stan learns a valuable lesson about love and family.
South Park's annual "Cow Days" party is happening! The cows become transfixed on a cow statue. In order to get the money they need to win Terrance and Phillip dolls, the boys sign Cartman up for a bull riding contest. A freak accident has Cartman believing he is a Vietnamese prostitute named Ming Li. The boys learn about money and cow insanity.
Chef is getting sued by Capitalist Records for trying to obtain the rights to a song he wrote twenty years ago. He needs 2 million dollars to hire Johnny Cochran. In response the boys round up all of Chef's old musician friends and organize a huge concert to raise the cash.
Sharon Marsh's Aunt Flo makes her monthly visit and she has present for Stan, a fish. Stan's fish really freaks him out, especially when the dead bodies start piling up. Mrs. Marsh is convinced Stan is doing the killings and begins hiding the bodies. The boys discover there are two Cartmans and a gateway to a parallel universe at the "Indian Burial Ground Pet Store."
Kyle, Stan and Kenny accompany Eric and his family to a Christmas celebration with the Cartman family. One of Cartman's relatives breaks out of jail for the reunion, with his cellmate, Charles Manson.
Harbucks coffee plans to move into South Park and drive Tweek coffee shop out of business. Mr. Garrison assigns a report on current events to help him keep his job. The boys are planning on doing their report on the underpants gnomes. Tweek's father schemes to use the boy's report as a platform for fighting Harbucks. The report the boys deliver sparks the town into taking action.
Kyle falls into a cave. Stan goes to rescue him and finds an iceman, and the two fight each other for sole credit. Dr. Mephisto discovers that the iceman has been frozen since 1996. The iceman is put on display and the fighting Kyle and Stan free him. The iceman tries to return to his family, but finds himself a man out of time. Meanwhile, the government has their own plans to use the iceman in their plot against Sweden.